[gmx-users] question about applying surface tension
Ali Shomali
ali.shomali111 at gmail.com
Fri May 12 17:44:52 CEST 2017
Dear Justin thanks for the answer
I think the surface tension line was deleted in email by mistake , sorry
for that. I managed to perform other simulations for DMPC and DPPC . in all
of them I applied reported surface tensions ( twice the reported surface
tension per interface) in all of them my area per lipid changes very
little and it's very confusing becuase I compared my mdp script with others
from internet , I'm sending my mdp options again (nstcomm is added):
title = NGT Equilibration for DPPC
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 1000000 ; 1000 ps (1 ns)
dt = 0.001 ; 2 fs
; Output control
nstxout = 10000 ; save coordinates every 0.2 ps
nstvout = 10000 ; save velocities every 0.2 ps
nstenergy = 100 ; save energies every 0.2 ps
nstlog = 100 ; update log file every 0.2 ps
; Neighborsearching
ns_type = grid ; search neighboring grid cels
nstlist = 10 ; 10 fs
rlist = 1.2 ; short-range neighborlist cutoff (in nm)
rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)
rvdw = 1.2 ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme_order = 4 ; cubic interpolation
; Temperature coupling is on
tcoupl = berendsen ; More accurate thermostat
tc-grps = DPPC SOL ; three coupling groups - more accurate
tau_t = 0.5 0.5 ; time constant, in ps
ref_t = 323 323 ; reference temperature, one for each group, in K
; Pressure coupling is on
pcoupl = berendsen ; Pressure coupling on in NPT
tau_p = 5.0 ; time constant, in ps
ref_p = 0 1.0 ; reference pressure, x-y, z (in bar)
compressibility = 4.5e-5 4.5e-5 ; isothermal compressibility, bar^-1
pcoupltype = surface-tension ;
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = no ; Velocity generation is off
; COM motion removal
; These options remove motion of the protein/bilayer relative to the
solvent/ions
nstcomm = 100
comm-mode = Linear
comm-grps = system
On Mon, May 8, 2017 at 4:38 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 5/7/17 2:56 PM, Ali Shomali wrote:
>
>> Thanks so much Justin for your answer. actually I performed different
>> simulations and compared the area per lipid with existing studies . for
>> example I used gromacs charmm 22 for DPPC simulation and compared the
>> results with Dr.Feller's paper. also I conducted a simulation on DMPC
>> membrane and compared the results with existing data from
>> doi:10.1021/jp048969n. also I performed a simulation with gromacs opls
>> force field on octadecanol monolayer and checked the results with
>> doi:10.1016/j.colsurfa.2012.09.025. in all of them my area per lipid
>> value
>> changes very little and another odd thing is that even when I apply a
>> large
>> surface tension , surface compresses!
>>
>
> You're sort of indirectly applying a surface tension. You've got an x-y
> pressure of 600 bar, which means the membrane will be squeezed under the
> influence of high pressure. Note that there are actual surface tension
> options that you should probably be using.
>
> -Justin
>
>
> I've tested all the option I could think of.
>> I would appreciate it so much if you can help me with this problem Justin
>> thanks again
>> Ali
>>
>> On Sun, May 7, 2017 at 10:34 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 5/6/17 6:58 PM, Ali Shomali wrote:
>>>
>>> Hello to all dear gromacs users
>>>>
>>>> I've faced a problem with applying surface tension , I'm , trying to
>>>> model
>>>> a monolayer and I've noticed whenever I apply a surface tension although
>>>> my
>>>> surface tension is converged my area per lipid is wrong . i managed to
>>>> model a bilayer to find out the problem and i noticed that in all my
>>>> simulations my area per lipid changes are very little no matter what is
>>>> surface tension nor cutoffs. but surface tension converges! i'm sending
>>>> my
>>>> mdp file .
>>>> I will be so thankful if some one helps
>>>>
>>>>
>>> Sounds like a force field issue. Which parameter set are you using, and
>>> do you have evidence that it should respond correctly under such
>>> conditions?
>>>
>>> -Justin
>>>
>>>
>>> mdp file :
>>>
>>>>
>>>> title = DMPC NPT equilibration
>>>> ; Run parameters
>>>> integrator = md ; leap-frog integrator
>>>> nsteps = 1000000 ; = 1000 ps
>>>> dt = 0.001 ; 1 fs
>>>> nstcomm = 10
>>>> comm-grps = SOL DMPC ; Remove COM for monolayers
>>>> separately
>>>> ; Output control
>>>> nstxout = 10000 ; save coordinates every 1.0 ps
>>>> nstvout = 10000 ; save velocities every 1.0 ps
>>>> nstenergy = 500 ; save energies every 1.0 ps
>>>> nstlog = 500 ; update log file every 1.0 ps
>>>>
>>>> ; Neighborsearching
>>>> cutoff-scheme = Verlet
>>>> ns_type = grid ; search neighboring grid cells
>>>> nstlist = 10 ; 20 fs, largely irrelevant with Verlet
>>>> rcoulomb = 1.4 ; short-range electrostatic cutoff (in nm)
>>>> rvdw = 1.4 ; short-range van der Waals cutoff (in nm)
>>>> ; Dispersion correction
>>>> DispCorr = EnerPres ; account for cut-off vdW scheme
>>>> ; Electrostatics
>>>> coulombtype = PME ; Particle Mesh Ewald for long-range
>>>> electrostatics
>>>> ; Temperature coupling is on
>>>> tcoupl = berendsen ; modified Berendsen thermostat
>>>> tc-grps = DMPC SOL ; two coupling groups - more accurate
>>>> tau_t = 0.1 0.1 ; time constant, in ps
>>>> ref_t = 330 330 ; reference temperature, one for each
>>>> group,
>>>> in K
>>>> ; Pressure coupling is on
>>>> Pcoupl = berendsen
>>>> tau_p = 10.0
>>>> compressibility = 4.5e-5 4.5e-5
>>>> ref_p = 600 1.0
>>>> ; Periodic boundary conditions
>>>> pbc = xyz ; 3-D PBC
>>>>
>>>>
>>>> --
>>> ==================================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 629
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>>
>>> ==================================================
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>>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
> --
> Gromacs Users mailing list
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